Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation

Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics

BACKGROUND

Molecular dynamics (MD) simulation is well-recognized as a powerful tool to investigate protein structure, function, and thermodynamics. MD simulation is also used to investigate high pressure effects on proteins. For conducting better MD simulation under high pressure, the main issues to be addressed are: (i) protein force fields and water models were originally developed to reproduce experimental properties obtained at ambient pressure; and (ii) the timescale to observe the pressure effect is often much longer than that of conventional MD simulations.

SCOPE OF REVIEW

First, we describe recent developments in MD simulation methodologies for studying the high-pressure structure and dynamics of protein molecules. These developments include force fields for proteins and water molecules, and enhanced simulation techniques. Then, we summarize recent studies of MD simulations of proteins in water under high pressure.

MAJOR CONCLUSIONS

Recent MD simulations of proteins in solution under pressure have reproduced various phenomena identified by experiments using high pressure, such as hydration, water penetration, conformational change, helix stabilization, and molecular stiffening.

GENERAL SIGNIFICANCE

MD simulations demonstrate differences in the properties of proteins and water molecules between ambient and high-pressure conditions. Comparing the results obtained by MD calculations with those obtained experimentally could reveal the mechanism by which biological molecular machines work well in collaboration with water molecules.

In silico characterization of protein partial molecular volumes and hydration shells

In this paper we present a computational approach, based on NVT molecular dynamics trajectories, that allows the direct evaluation of the protein partial molecular volume. The results obtained for five different globular proteins demonstrate the accuracy of this computational procedure in reproducing protein partial molecular volumes, providing quantitative characterization of the hydration shell in terms of the protein excluded volume, hydration shell ellipsoidal volume and related solvent density. Remarkably, our data indicate for the hydration shell a ≈10% solvent density increase with respect to the liquid water bulk density, in excellent agreement with the available experimental data.

The unfolding effects on the protein hydration shell and partial molar volume: a computational study

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes.

Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation

Water plays a unique role in all living organisms. Not only is it nature's ubiquitous solvent, but it also actively takes part in many cellular processes. In particular, the structure and properties of interfacial water near biomolecules such as proteins are often related to the function of the respective molecule. It can therefore be highly instructive to study the local water density around solutes in cellular systems, particularly when solvent-mediated forces such as the hydrophobic effect are relevant. Computational methods such as molecular dynamics (MD) simulations seem well suited to study these systems at the atomic level. However, due to sampling requirements, it is not clear that MD simulations are, indeed, the method of choice to obtain converged densities at a given level of precision. We here compare the calculation of local water densities with two different methods: MD simulations and the three-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH). In particular, we investigate the convergence of the local water density to assess the required simulation times for different levels of resolution. Moreover, we provide a quantitative comparison of the densities calculated with MD and with 3D-RISM-KH and investigate the effect of the choice of the water model for both methods. Our results show that 3D-RISM-KH yields density distributions that are very similar to those from MD up to a 0.5 Å resolution, but for significantly reduced computational cost. The combined use of MD and 3D-RISM-KH emerges as an auspicious perspective for efficient solvent sampling in dynamical systems.

Probing the effect of water-water interactions on enzyme activity with salt gradients: a case-study using ribonuclease t1

Water molecules interact with one another via hydrogen bonds. Experimental and theoretical evidence indicates that these hydrogen bonds occur in two modalities--high- and low-angle hydrogen bonding--and that the addition of various solutes to water affects only the number of water molecules participating in a specific type of hydrogen bond interactions, not the nature of the water-water interactions. In this work, we have investigated the effect of each of these hydrogen bonding types upon the activity of the enzyme ribonuclease t1. This was done through perturbation of the water hydrogen bonding distribution by using various salts. Our results indicate that various salts differ in their ability to reduce the enzymatic activity of ribonuclease t1, and this ability is well correlated with the ability of each salt to promote high-angle hydrogen bonding in water. By applying the two-phase model of liquid water (i.e., liquid water being modeled as an equilibrium existing between two phases, LD and HD water), we demonstrate that our results are compatible with the assumption that increasing the population of high-angle hydrogen bonds among water molecules stabilizes the more compact, less active conformations of the enzyme. This indicates that the structures that proteins adopt in water solution depend upon the nature of interactions between water molecules.

Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber

We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package, and is illustrated here on alanine dipeptide and protein G.

Hydration effects on the HET-s prion and amyloid-beta fibrillous aggregates, studied with three-dimensional molecular theory of solvation

We study the thermodynamic properties of the experimental fragments of the amyloid fibril made of the HET-s prion proteins (the infectious element of the filamentous fungus Podospora anserina) and of amyloid-beta proteins (the major component of Alzheimer's disease-associated plaques) by using the three-dimensional molecular theory of solvation. The full quantitative picture of hydration effects, including the hydration thermodynamics and hydration structure around the fragments, is presented. For both the complexes, the hydration entropic effects dominate, which results in the entropic part offsetting the unfavorable energetic part of the free energy change upon the association. This is in accord with the fact that the hydrophobic cooperativity plays an essential role in the formation of amyloid fibrils. By calculating the partial molar volume of the proteins, we found that the volume change upon the association in both the systems is large and positive, with the implication that high pressure causes destabilization of the fibril. This observation is in good agreement with the recent experimental results. We also found that both the HET-s and amyloid-beta pentamers have loose intermolecular packing with voids. The three-dimensional molecular theory of solvation predicts that water molecules can be locked in the interior cavities along the fibril axis for both the HET-s and amyloid-beta proteins. We provide a detailed molecular picture of the structural water localized in the interior of the fibrils. Our results suggest that the interior hydration plays an important role in the structural stability of fibrils.

Three-dimensional distribution function theory for the prediction of protein-ligand binding sites and affinities: application to the binding of noble gases to hen egg-white lysozyme in aqueous solution

The three-dimensional distribution function theory of molecular liquids is applied to lysozyme in mixtures of water and noble gases. The results indicate that the theory has the capability of predicting the protein-ligand binding sites and affinities. First, it is shown that the theory successfully reproduces the binding sites of xenon found by X-ray crystallography. Then, the ability of the theory to predict the size selectivity of noble gases is demonstrated. The effect of water on the selectivity is clarified by a theoretical analysis. Finally, it is demonstrated that the dose-response curve, which is employed in experiments for examining the binding affinity, is realized by the theory.

Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin

The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier.